def test_hsolve_calcium():
for tick in range(0, 7):
moose.setClock(tick, 10e-6)
moose.setClock(8, 0.005)
lib = moose.Neutral('/library')
model = moose.loadModel(p_file, 'neuron')
assert model, model
pulse = moose.PulseGen('/neuron/pulse')
inject = 100e-10
chan_proto.chan_proto('/library/SK', param_chan.SK)
chan_proto.chan_proto('/library/CaL12', param_chan.Cal)
pulse.delay[0] = 8.
pulse.width[0] = 500e-12
pulse.level[0] = inject
pulse.delay[1] = 1e9
for comp in moose.wildcardFind('/neuron/#[TYPE=Compartment]'):
new_comp = moose.element(comp)
new_comp.initVm = -.08
difs, difb = td.add_difshells_and_buffers(new_comp, difshell_no,
difbuf_no)
for name in cond:
chan = td.addOneChan(name, cond[name], new_comp)
if 'Ca' in name:
moose.connect(chan, "IkOut", difs[0], "influx")
if 'SK' in name:
moose.connect(difs[0], 'concentrationOut', chan, 'concen')
data = moose.Neutral('/data')
vmtab = moose.Table('/data/Vm')
shelltab = moose.Table('/data/Ca')
caltab = moose.Table('/data/CaL_Gk')
sktab = moose.Table('/data/SK_Gk')
moose.connect(vmtab, 'requestOut', moose.element('/neuron/soma'), 'getVm')
moose.connect(shelltab, 'requestOut', difs[0], 'getC')
moose.connect(caltab, 'requestOut', moose.element('/neuron/soma/CaL12'),
'getGk')
moose.connect(sktab, 'requestOut', moose.element('/neuron/soma/SK'),
'getGk')
hsolve = moose.HSolve('/neuron/hsolve')
hsolve.dt = 10e-6
hsolve.target = ('/neuron/soma')
t_stop = 10.
moose.reinit()
moose.start(t_stop)
vec1 = sktab.vector
vec2 = shelltab.vector
assert_stat(vec1, [0.0, 5.102834e-22, 4.79066e-22, 2.08408e-23])
assert_stat(vec2, [5.0e-5, 5.075007e-5, 5.036985e-5, 2.1950117e-7])
assert len(np.where(sktab.vector < 1e-19)[0]) == 2001
assert len(np.where(shelltab.vector > 50e-6)[0]) == 2000
def test_diffshell():
lib = moose.Neutral('/library')
for tick in range(0, 7):
moose.setClock(tick, dt)
moose.setClock(8, 0.005) # set output clock
model = moose.Neutral('/model')
dend = moose.Compartment('/model/dend')
pulse = moose.PulseGen('/model/pulse')
data = moose.Neutral('/data')
vmtab = moose.Table('/data/dend_Vm')
gktab = moose.Table('/data/CaT_Gk')
iktab = moose.Table('/data/CaT_Ik')
dend.Cm = Cm
dend.Rm = Rm
dend.Em = Em
dend.initVm = Vm_0
dend.diameter = dend_diameter
dend.length = dend_length
pulse.delay[0] = 8.
pulse.width[0] = 500e-3
pulse.level[0] = inject
pulse.delay[1] = 1e9
chan = chan_proto.chan_proto('/library/CaL12', param_chan.Cal)
m = moose.connect(pulse, 'output', dend, 'injectMsg')
moose.connect(vmtab, 'requestOut', dend, 'getVm')
chan = addOneChan('CaL12', gbar, dend)
moose.connect(gktab, 'requestOut', chan, 'getGk')
moose.connect(iktab, 'requestOut', chan, 'getIk')
diftab = []
buftab = []
difs, difb = add_difshells_and_buffers(dend, difshell_no, difbuff_no)
if pumps:
pump = moose.MMPump('/model/dend/pump')
pump.Vmax = kcat
pump.Kd = km
moose.connect(pump, "PumpOut", difs[0], "mmPump")
if difs:
moose.connect(chan, "IkOut", difs[0], "influx")
moose.connect(difs[0], 'concentrationOut', chan, 'concen')
for i, dif in enumerate(difs):
res_dif = moose.Table('/data/' + difshell_name + str(i))
diftab.append(res_dif)
moose.connect(diftab[i], 'requestOut', dif, 'getC')
if (difbuff_no):
buftab.append([])
for j, buf in enumerate(difb[i]):
res_buf = moose.Table('/data/' + difshell_name + str(i) + '_' +
difbuff_name + str(j))
buftab[i].append(res_buf)
moose.connect(buftab[i][j], 'requestOut', buf, 'getBBound')
moose.reinit()
if not gbar:
for i, dif in enumerate(difs):
if i == 0:
dif.C = Ca_initial
else:
dif.C = 0
for j, dbuf in enumerate(difb[i]):
dbuf.bFree = dbuf.bTot
moose.start(t_stop)
t = np.linspace(0, t_stop, len(vmtab.vector))
fname = 'moose_results_difshell_no_' + str(
difshell_no) + '_difbuffer_no_' + str(difbuff_no) + '_pump_' + str(
pumps) + '_gbar_' + str(gbar) + '.txt'
header = 'time Vm Ik Gk'
number = 4 + difshell_no * (difbuff_no + 1)
res = np.zeros((len(t), number))
res[:, 0] = t
res[:, 1] = vmtab.vector
res[:, 2] = iktab.vector
res[:, 3] = gktab.vector
for i in range(difshell_no):
header += ' difshell_' + str(i)
res[:, 4 + i * (difbuff_no + 1)] = diftab[i].vector
if (difbuff_no):
for j, buf in enumerate(buftab[i]):
res[:, 4 + i * (difbuff_no + 1) + j + 1] = buf.vector
header += ' difshell_' + str(i) + '_difbuff_' + str(j)
np.savetxt(fname, res, header=header, comments='')
mean, std = np.mean(vec), np.std(vec)
computed = [min_, max_, mean, std]
assert np.allclose( computed, expected ), \
"Got %s expected %s" % (computed, expected)
if __name__ == '__main__':
for tick in range(0, 7):
moose.setClock(tick, 10e-6)
moose.setClock(8, 0.005)
lib = moose.Neutral('/library')
model = moose.loadModel(p_file, 'neuron')
pulse = moose.PulseGen('/neuron/pulse')
inject = 100e-10
chan_proto.chan_proto('/library/SK', param_chan.SK)
chan_proto.chan_proto('/library/CaL12', param_chan.Cal)
pulse.delay[0] = 8.
pulse.width[0] = 500e-12
pulse.level[0] = inject
pulse.delay[1] = 1e9
for comp in moose.wildcardFind('/neuron/#[TYPE=Compartment]'):
new_comp = moose.element(comp)
new_comp.initVm = -.08
difs, difb = td.add_difshells_and_buffers(new_comp, difshell_no,
difbuf_no)
for name in cond:
chan = td.addOneChan(name, cond[name], new_comp)
if 'Ca' in name:
moose.connect(chan, "IkOut", difs[0], "influx")
gktab = moose.Table('/data/CaT_Gk')
iktab = moose.Table('/data/CaT_Ik')
dend.Cm = Cm
dend.Rm = Rm
dend.Em = Em
dend.initVm = Vm_0
dend.diameter = dend_diameter
dend.length = dend_length
pulse.delay[0] = 8.
pulse.width[0] = 500e-3
pulse.level[0] = inject
pulse.delay[1] = 1e9
chan = chan_proto.chan_proto('/library/CaL12',param_chan.Cal)
m = moose.connect(pulse, 'output', dend, 'injectMsg')
moose.connect(vmtab, 'requestOut', dend, 'getVm')
chan = addOneChan('CaL12', gbar, dend)
moose.connect(gktab, 'requestOut', chan, 'getGk')
moose.connect(iktab, 'requestOut', chan, 'getIk')
diftab = []
buftab = []
difs, difb = add_difshells_and_buffers(dend,difshell_no,difbuff_no)
if pumps:
pump = moose.MMPump('/model/dend/pump')
pump.Vmax = kcat
pump.Kd = km
moose.connect(pump, "PumpOut", difs[0], "mmPump")
if difs:
moose.connect(chan, "IkOut", difs[0], "influx")
gktab = moose.Table('/data/CaT_Gk')
iktab = moose.Table('/data/CaT_Ik')
dend.Cm = Cm
dend.Rm = Rm
dend.Em = Em
dend.initVm = Vm_0
dend.diameter = dend_diameter
dend.length = dend_length
pulse.delay[0] = 8.
pulse.width[0] = 500e-3
pulse.level[0] = inject
pulse.delay[1] = 1e9
chan = chan_proto.chan_proto('/library/CaL12',param_chan.Cal)
m = moose.connect(pulse, 'output', dend, 'injectMsg')
moose.connect(vmtab, 'requestOut', dend, 'getVm')
chan = addOneChan('CaL12', gbar, dend)
moose.connect(gktab, 'requestOut', chan, 'getGk')
moose.connect(iktab, 'requestOut', chan, 'getIk')
diftab = []
buftab = []
difs, difb = add_difshells_and_buffers(dend,difshell_no,difbuff_no)
if pumps:
pump = moose.MMPump('/model/dend/pump')
min_, max_ = np.min( vec ), np.max( vec )
mean, std = np.mean( vec ), np.std( vec )
computed = [ min_, max_, mean, std ]
assert np.allclose( computed, expected ), \
"Got %s expected %s" % (computed, expected)
if __name__ =='__main__':
for tick in range(0, 7):
moose.setClock(tick,10e-6)
moose.setClock(8, 0.005)
lib = moose.Neutral('/library')
model = moose.loadModel(p_file,'neuron')
pulse = moose.PulseGen('/neuron/pulse')
inject = 100e-10
chan_proto.chan_proto('/library/SK',param_chan.SK)
chan_proto.chan_proto('/library/CaL12',param_chan.Cal)
pulse.delay[0] = 8.
pulse.width[0] = 500e-12
pulse.level[0] = inject
pulse.delay[1] = 1e9
for comp in moose.wildcardFind('/neuron/#[TYPE=Compartment]'):
new_comp = moose.element(comp)
new_comp.initVm = -.08
difs, difb = td.add_difshells_and_buffers(new_comp,difshell_no,difbuf_no)
for name in cond:
chan = td.addOneChan(name,cond[name],new_comp)
if 'Ca' in name:
moose.connect(chan, "IkOut", difs[0], "influx")